Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries

Mechanistic Insights from the Crystal Structure and Computational Analysis of the Radical SAM Deaminase DesII

Radical S-adenosyl-L-methionine (SAM) enzymes couple the reductive cleavage of SAM to radical-mediated transformations that have proven to be quite broad in scope. DesII is one such enzyme from the biosynthetic pathway of TDP-desosamine where it catalyzes a radical-mediated deamination. Previous studies have suggested that this reaction proceeds via direct elimination of ammonia from an α-hydroxyalkyl radical or its conjugate base (i.e., a ketyl radical) rather than 1,2-migration of the amino group to form a carbinolamine radical intermediate. However, without a crystal structure, the active site features responsible for this chemistry have remained largely unknown. The crystallographic studies described herein help to fill this gap by providing a structural description of the DesII active site. Computational analyses based on the solved crystal structure are consistent with direct elimination and indicate that an active site glutamate residue likely serves as a general base to promote deprotonation of the α-hydroxyalkyl radical intermediate and elimination of the ammonia group.

Reactivity Tracking of an Enzyme Progress Coordinate

The reactivity of individual solvent-coupled protein configurations is used to track and resolve the progress coordinate for the core reaction sequence of substrate radical rearrangement and hydrogen atom transfer in the ethanolamine ammonia-lyase (EAL) enzyme from Salmonella enterica. The first-order decay of the substrate radical intermediate is the monitored reaction. Heterogeneous confinement from sucrose hydrates in the mesophase solvent surrounding the cryotrapped protein introduces distributed kinetics in the non-native decay of the substrate radical pair capture substate, which arise from an ensemble of configurational microstates. Reaction rates increase by >103-fold across the distribution to approach that for the native enabled substate for radical rearrangement, which reacts with monotonic kinetics. The native progress coordinate thus involves a collapse of the configuration space to generate optimized reactivity. Reactivity tracking reveals fundamental features of solvent-protein-reaction configurational coupling and leads to a model that refines the ensemble paradigm of enzyme catalysis for strongly adiabatic chemical steps.

Structural Insights into the Very Low Activity of the Homocoenzyme B12 Adenosylmethylcobalamin in Coenzyme B12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase

The X-ray structures of coenzyme B12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH2 group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.

Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase

Coenzyme B₁₂ (adenosylcobalamin) -dependent ethanolamine ammonia-lyase (EAL) is the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. The enzyme conducts a complex choreography of bond-making/bond-breaking steps that rearrange substrate to products through a radical mechanism, with themes common to other coenzyme B₁₂-dependent and radical enzymes. The methods presented are targeted to test the hypothesis that particular, select protein and coupled solvent configurational fluctuations contribute to enzyme function. The general approach is to correlate enzyme function with an introduced perturbation that alters the properties (for example, degree of concertedness, or collectiveness) of protein and coupled solvent dynamics. Methods for sample preparation and low-temperature kinetic measurements by using temperature-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy are detailed. A framework for interpretation of results obtained in ensemble systems under conditions of statistical equilibrium within the reacting, globally unstable state is presented. The temperature-dependence of the first-order rate constants for decay of the cryotrapped paramagnetic substrate radical state in EAL, through the chemical step of radical rearrangement, displays a piecewise-continuous Arrhenius dependence from 203 to 295K, punctuated by a kinetic bifurcation over 219-220K. The results reveal the obligatory contribution of a class of select collective protein and coupled solvent fluctuations to the interconversion of two resolved, sequential configurational substates, on the decay time scale. The select class of collective fluctuations also contributes to the chemical step. The methods and analysis are generally applicable to other coenzyme B₁₂-dependent and related radical enzymes.

Deuterium Kinetic Isotope Effects Resolve Low-Temperature Substrate Radical Reaction Pathways and Steps in B12-Dependent Ethanolamine Ammonia-Lyase

The first-order reaction kinetics of the cryotrapped 1,1,2,2-²H₄-aminoethanol substrate radical intermediate state in the adenosylcobalamin (B₁₂)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella enterica serovar Typhimurium are measured over the range of 203-225 K by using time-resolved, full-spectrum electron paramagnetic resonance spectroscopy. The studies target the fundamental understanding of the mechanism of EAL, the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. Incorporation of ²H into the hydrogen transfer that follows the substrate radical rearrangement step in the substrate radical decay reaction sequence leads to an observed ¹H/²H isotope effect of approximately 2 that preserves, with high fidelity, the idiosyncratic piecewise pattern of rate constant versus inverse temperature dependence that was previously reported for the ¹H-labeled substrate, including a monoexponential regime (T ≥ 220 K) and two distinct biexponential regimes (T = 203-219 K). In the global kinetic model, reaction at ≥220 K proceeds from the substrate radical macrostate, S^•, and at 203-219 K along parallel pathways from the two sequential microstates, S₁^• and S₂^•, that are distinguished by different protein configurations. Decay from S^•, or S₁^• and S₂^•, is rate-determined by radical rearrangement (¹H) or by contributions from both radical rearrangement and hydrogen transfer (²H). Non-native direct decay to products from S₁^• is a consequence of the free energy barrier to the native S₁^• → S₂^• protein configurational transition. At physiological temperatures, this is averted by the fast protein configurational dynamics that guide the S₁^• → S₂^• transition.

Mechanistic Implications of the Deamination of TDP-4-amino-4-deoxy-d-fucose Catalyzed by the Radical SAM Enzyme DesII

DesII is a radical SAM lyase that catalyzes a deamination reaction during the biosynthesis of desosamine in Streptomyces venezuelae. Competing mechanistic hypotheses for this radical-mediated reaction are differentiated according to whether a 1,2-migration takes place and the timing of proton abstraction following generation of a substrate α-hydroxyalkyl radical intermediate. In this study, the deuterated C4 epimer of the natural substrate, TDP-4-amino-4-deoxy-d-[3-²H]fucose, was prepared and shown to be a substrate for DesII undergoing deamination alone with a specific activity that is only marginally reduced (∼3-fold) with respect to that of deamination of the natural substrate. Furthermore, pH titration of the deamination reaction implicates the presence of a hydron acceptor that facilitates catalysis but does not appear to be necessary. On the basis of these as well as previously reported results, a mechanism involving direct elimination of ammonium with concerted proton transfer to the nucleofuge from the adjacent α-hydroxyalkyl radical is proposed.

Two Dynamical Regimes of the Substrate Radical Rearrangement Reaction in B12-Dependent Ethanolamine Ammonia-Lyase Resolve Contributions of Native Protein Configurations and Collective Configurational Fluctuations to Catalysis

The kinetics of the substrate radical rearrangement reaction step in B₁₂-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium are measured over a 92 K temperature range. The observed first-order rate constants display a piecewise-continuous Arrhenius dependence, with linear regions over 295 → 220 K (monoexponential) and 214 → 203 K (biexponential) that are delineated by a kinetic bifurcation and kinks at 219 and 217 K, respectively. The results are interpreted by using a free energy landscape model and derived microscopic kinetic mechanism. The bifurcation and kink transitions correspond to the effective quenching of two distinct sets of native collective protein configurational fluctuations that (1) reconfigure the protein within the substrate radical free energy minimum, in a reaction-enabling step, and (2) create the protein configurations associated with the chemical step. Below 217 K, the substrate radical decay reaction persists. Increases in activation enthalpy and entropy of both the microscopic enabling and reaction steps indicate that this non-native reaction coordinate is conducted by local, incremental fluctuations. Continuity in the Arrhenius relations indicates that the same sets of protein groups and interactions mediate the rearrangement over the 295 to 203 K range, but with a repertoire of configurations below 217 K that is restricted, relative to the native configurations accessible above 219 K. The experimental features of a culled reaction step, first-order kinetic measurements, and wide room-to-cryogenic temperature range, allow the direct demonstration and kinetic characterization of protein dynamical contributions to the core adiabatic, bond-making/bond-breaking reaction in EAL.

Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems

Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.

Kinetic isolation and characterization of the radical rearrangement step in coenzyme B12-dependent ethanolamine ammonia-lyase

The transient decay reaction kinetics of the 1,1,2,2-(2)H(4)-aminoethanol generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium have been measured by using time-resolved, full-spectrum X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy in frozen aqueous solution over the temperature range of 190-207 K. The decay reaction involves sequential passage through the rearrangement step [substrate radical --> product radical] and the step [product radical --> diamagnetic product] that involves hydrogen atom transfer (HT) from carbon C5' of the adenosine moiety of the cofactor to the product radical C2 center. As found for the (1)H-substrate radical [Zhu, C.; Warncke, K. Biophys. J. 2008, 95, 5890], the decay kinetics for the (2)H-substrate radical over 190-207 K represent two noninteracting populations (fast decay population: normalized amplitude = 0.44 +/- 0.07; observed rate constant, k(obs,f) = 5.3 x 10(-5)-1.1 x 10(-3) s(-1); slow decay population: k(obs,s) = 6.1 x 10(-6)-2.9 x 10(-4) s(-1)). The (1)H/(2)H isotope effects (IE) for the fast and slow decay reactions are 1.4 +/- 0.2 and 0.79 +/- 0.11, respectively. The IE on the fast phase is uniform over the temperature interval, and the value is consistent with an alpha-secondary hydrogen kinetic IE, which arises from changes in the force constants of the C-H bonds in the substrate radical structure, upon passing from the substrate radical state to the rearrangement transition state. Therefore, we propose that k(obs,f) represents the rate constant for the radical rearrangement and that this step is the rate-determining step in substrate radical decay. The Arrhenius activation energy for the (1)H-substrate radical rearrangement (13.5 +/- 0.4 kcal/mol) is consistent with values from quantum chemical calculations performed on simple models. The results show that the core, radical rearrangement reaction is culled from the catalytic cycle in the low-temperature system, thus establishing the system for detailed transient kinetic and spectroscopic analysis of protein structural and dynamic contributions to EAL catalysis.

Modeling the reactions catalyzed by coenzyme B12-dependent enzymes

Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained catalysis depends on a delicate energy balance. Radical-based enzyme reactions are often difficult to probe experimentally, so theoretical investigations have a particularly valuable role to play in their study. Our research demonstrates that a small-model approach can provide important and revealing insights into the mechanism of action of AdoCbl-dependent enzymes.

Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K

The decay kinetics of the aminoethanol-generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10(5) s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 < or = T < or = 207 K: the decay is biexponential with constant fast (0.57 +/- 0.04) and slow (0.43 +/- 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T > or = 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k(obs,m)) and the fast phase of the biexponential decay (k(obs,f)) adhere to the same linear relation on an lnk versus T(-1) (Arrhenius) plot. Thus, k(obs,m) and k(obs,f) correspond to the same apparent Arrhenius prefactor and activation energy (logA(app,f) (s(-1)) = 13.0, E(a,app,f) = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k(obs,m) and k(obs,f) represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k(obs,s)) for 190 < or = T < or = 207 K obeys a different linear Arrhenius relation (logA(app,s) (s(-1)) = 13.9, E(a,app,s) = 16.6 kcal/mol). In the transition temperature range, k(obs,s) displays a super-Arrhenius increase with increasing temperature. The change in E(a,app,s) with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co(II)-substrate radical pair lies below 190 K.

Kinetic and thermodynamic characterization of Co(II)-substrate radical pair formation in coenzyme B12-dependent ethanolamine ammonia-lyase in a cryosolvent system by using time-resolved, full-spectrum continuous-wave electron paramagnetic resonance spectroscopy

The formation of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12 (adenosylcobalamin)-dependent ethanolamine ammonia-lyase (EAL) from Salmonella typhimurium has been studied by using time-resolved continuous-wave electron paramagnetic resonance (EPR) spectroscopy in a cryosolvent system. The 41% v/v DMSO/water cryosolvent allows mixing of holoenzyme and substrate, (S)-2-aminopropanol, at 230 K under conditions of kinetic arrest. Temperature step from 230 to 234-248 K initiates the cleavage of the cobalt-carbon bond and the monoexponential rise (rate constant, k(obs) = tau(obs)(-1)) of the EPR-detected Co(II)-substrate radical pair state. The detection deadtime: tau(obs) ratio is reduced by >10(2), relative to millisecond rapid mixing experiments at ambient temperatures. The EPR spectrum acquisition time is <tau(obs), which allows continuous acquisition of spectra during progress of the reaction. The k(obs) values and Co(II)-substrate radical pair amplitudes are independent of substrate concentration at each temperature. Therefore, the reaction occurs from the enzyme x coenzyme x substrate ternary complex. The constant value of the Co(II)-substrate radical pair amplitude at reaction times >5tau(obs), the approximately 10(2)-fold slower rate of the substrate radical rearrangement reaction relative to k(obs), and the reversible temperature dependence of the amplitude indicate that the Co(II)-substrate radical pair and ternary complex are essentially at equilibrium. The reaction is thus treated as a relaxation to equilibrium by using a linear two-step, three-state mechanism. The intermediate state in this mechanism, the Co(II)-5'-deoxyadenosyl radical pair, is not detected by EPR at signal-to-noise ratios of 10(3), which indicates that the free energy of the Co(II)-5'-deoxyadenosyl radical pair state is >3.3 kcal/mol, relative to the Co(II)-substrate radical pair. Van't Hoff analysis yields DeltaH13 = 10.8 +/- 0.8 kcal/mol and DeltaS13 = 45 +/- 3 cal/mol/K for the transition from the ternary complex to the Co(II)-substrate radical pair state. The free energy difference, DeltaG13, is zero to within one standard deviation over the temperature range 234-248 K. The extrapolated value of DeltaG13 at 298 K is -2.6 +/- 1.2 kcal/mol. The estimated EAL protein-associated contribution to the free energy difference is DeltaG(EAL) = -24 kcal/mol at 240 K, and DeltaH(EAL) = -13 kcal/mol and DeltaS(EAL) = 38 cal/mol/K. The results show that the EAL protein makes both strong enthalpic and entropic contributions to overcome the large, unfavorable cobalt-carbon bond dissociation energy, which biases the reaction in the forward direction of Co-C bond cleavage and Co(II)-substrate radical pair formation.

Stabilisation of methylene radicals by cob(II)alamin in coenzyme B12 dependent mutases

Coenzyme B12 initiates radical chemistry in two types of enzymatic reactions, the irreversible eliminases (e.g., diol dehydratases) and the reversible mutases (e.g., methylmalonyl-CoA mutase). Whereas eliminases that use radical generators other than coenzyme B12 are known, no alternative coenzyme B12 independent mutases have been detected for substrates in which a methyl group is reversibly converted to a methylene radical. We predict that such mutases do not exist. However, coenzyme B12 independent pathways have been detected that circumvent the need for glutamate, beta-lysine or methylmalonyl-CoA mutases by proceeding via different intermediates. In humans the methylcitrate cycle, which is ostensibly an alternative to the coenzyme B12 dependent methylmalonyl-CoA pathway for propionate oxidation, is not used because it would interfere with the Krebs cycle and thereby compromise the high-energy requirement of the nervous system. In the diol dehydratases the 5'-deoxyadenosyl radical generated by homolysis of the carbon-cobalt bond of coenzyme B12 moves about 10 A away from the cobalt atom in cob(II)alamin. The substrate and product radicals are generated at a similar distance from cob(II)alamin, which acts solely as spectator of the catalysis. In glutamate and methylmalonyl-CoA mutases the 5'-deoxyadenosyl radical remains within 3-4 A of the cobalt atom, with the substrate and product radicals approximately 3 A further away. It is suggested that cob(II)alamin acts as a conductor by stabilising both the 5'-deoxyadenosyl radical and the product-related methylene radicals.

Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a beta8alpha8, TIM-barrel fold and radical catalytic site structural features

The structure of the EutB protein from Salmonella typhimurium, which contains the active site of the coenzyme B12 (adenosylcobalamin)-dependent enzyme, ethanolamine ammonia-lyase, has been predicted by using structural proteomics techniques of comparative modelling. The 453-residue EutB protein displays no significant sequence identity with proteins of known structure. Therefore, secondary structure prediction and fold recognition algorithms were used to identify templates. Multiple three-dimensional template matching (threading) servers identified predominantly beta8alpha8, TIM-barrel proteins, and in particular, the large subunits of diol dehydratase (PDB: 1eex:A, 1dio:A) and glycerol dehydratase (PDB: 1mmf:A), as templates. Consistent with this identification, the dehydratases are, like ethanolamine ammonia-lyase, Class II coenzyme B12-dependent enzymes. Model building was performed by using MODELLER. Models were evaluated by using different programs, including PROCHECK and VERIFY3D. The results identify a beta8alpha8, TIM-barrel fold for EutB. The beta8alpha8, TIM-barrel fold is consistent with a central role of the alpha/beta-barrel structures in radical catalysis conducted by the coenzyme B12- and S-adenosylmethionine-dependent (radical SAM) enzyme superfamilies. The EutB model and multiple sequence alignment among ethanolamine ammonia-lyase, diol dehydratase, and glycerol dehydratase from different species reveal the following protein structural features: (1) a "cap" loop segment that closes the N-terminal region of the barrel, (2) a common cobalamin cofactor binding topography at the C-terminal region of the barrel, and (3) a beta-barrel-internal guanidinium group from EutB R160 that overlaps the position of the active-site potassium ion found in the dehydratases. R160 is proposed to have a role in substrate binding and radical catalysis.

Divergent mechanisms of suicide inactivation for ethanolamine ammonia-lyase

Ab initio molecular orbital calculations have been used to study the mechanism of suicide inactivation of ethanolamine ammonia-lyase induced by three different substrate analogues. Analysis of the normal catalytic mechanism with 2-aminoethanol (ethanolamine) as substrate predicts that both the hydrogen-abstraction and hydrogen-reabstraction steps involving the B(12)-cofactor are likely to be exothermic. On the other hand, the proposed inactivation mechanism for the first substrate analogue, glycolaldehyde, leads to a highly stabilized radical that results in a very endothermic (by ca. 90 kJ mol(-)(1)) hydrogen-reabstraction step, which is thought to halt the normal function of the enzyme. Curiously, the energy requirements for a catalytically imposed mechanism in the case of the second substrate analogue, 2-hydroxyethylhydrazine (HEH), parallel those for the catalytic substrate, despite the fact that HEH is found to inactivate EAL experimentally. However, further analysis reveals the presence of a lower energy pathway for HEH that leads to the formation of the highly stabilized hydrazinium radical cation. In a manner similar to when glycolaldehyde is the substrate analogue, this results in an endothermicity for the hydrogen-reabstraction step that is prohibitively large. In contrast to these related inactivation mechanisms, the third substrate analogue, 2-aminoacetaldehyde, apparently accomplishes the inactivation of EAL in an entirely different manner. A pathway for the experimentally observed formation of acetic acid and ammonium cation has been identified and appears catalytic in the sense that 5'-deoxyadenosyl radical is regenerated. However, mechanisms to account for the subsequent formation of 4',5'-anhydroadenosine and degradation of the corrinoid ring of the cofactor have not been elucidated.

Catalytic Roles of Active-Site Amino Acid Residues of Coenzyme B12-Dependent Diol Dehydratase: Protonation State of Histidine and Pull Effect of Glutamate

The hydrogen abstraction and the OH migration processes catalyzed by diol dehydratase are discussed by means of a quantum mechanical/molecular mechanical method. To evaluate the push effect of His143 and the pull effect of Glu170, we considered three kinds of whole-enzyme model, the protonated and two unprotonated His143 models. A calculated activation energy for the hydrogen abstraction by the adenosyl radical is 15.6 (13.6) kcal/mol in the protonated (unprotonated) His143 model. QM/MM calculational results show that the mechanism of the OH migration is significantly changed by the protonation of His143. In the protonated His143 model, the OH group migration triggered by the full proton donation from the imidazolium to the migrating OH group occurs by a stepwise OH abstraction/re-addition process in which the water production reduces the barrier for the C-O bond cleavage. On the other hand, the OH migration in the unprotonated His143 model proceeds in a concerted manner, as we previously proposed using a simple model including only K+ ion and substrate. The latter mechanism seems to be kinetically more favorable from the calculated energy profiles and is consistent with experimental results. The activation barrier of the OH group migration step is only 1.6 kcal/mol reduced by the hydrogen-bonding interaction between the O2 of the substrate and unprotonated His143. Thus, it is predicted that His143 is not protonated, and therefore the main active-site amino acid residue that lowers the energy of the transition state for the OH group migration is determined to be Glu170.

The eutD gene of Salmonella enterica encodes a protein with phosphotransacetylase enzyme activity

The EutD protein of Salmonella enterica is homologous to the catalytic domain of the phosphotransacetylase (Pta) enzyme. The Pta-like activity level of the EutD enzyme compared favorably to that of other Pta enzymes. High-pressure liquid chromatography and mass spectrometry verified that acetyl-coenzyme A was the product of the reaction. The EutD protein restored growth of an S. enterica pta strain on acetate as the source of carbon and energy.